recipe cnv_facets

Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data

Homepage:

https://github.com/dariober/cnv_facets

License:

MIT / MIT

Recipe:

/cnv_facets/meta.yaml

package cnv_facets

versions:

0.16.1-1,  0.16.1-0,  0.16.0-1,  0.16.0-0,  0.15.0-1,  0.15.0-0,  0.14.0-1,  0.13.0-1,  0.12.1-1, 

0.16.1-1,  0.16.1-0,  0.16.0-1,  0.16.0-0,  0.15.0-1,  0.15.0-0,  0.14.0-1,  0.13.0-1,  0.12.1-1,  0.12.1-0,  0.12.0-0,  v0.11.3-2,  v0.11.3-1,  v0.11.2-1

depends bcftools:

>=1.21,<2.0a0

depends bcftools:

>=1.9

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends htslib:

>=1.21,<1.22.0a0

depends libgcc:

>=12

depends libgfortran:

depends libgfortran5:

>=12.4.0

depends libstdcxx:

>=12

depends python:

>=3.12,<3.13.0a0

depends r-argparse:

>=2.1.6

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-facets:

>=0.6.2,<1.0a0

depends r-ggplot2:

depends r-gridextra:

depends r-jsonlite:

depends samtools:

>=1.21,<2.0a0

depends snp-pileup:

>=0.6.2,<0.7.0a0

requirements:

additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install cnv_facets

and update with::

   mamba update cnv_facets

To create a new environment, run:

mamba create --name myenvname cnv_facets

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/cnv_facets:<tag>

(see `cnv_facets/tags`_ for valid values for ``<tag>``)

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